Hair Direction in Cycles ParticleSystem
The object origin of the cylinder is used as the emission point. In your .blend,  the origin of the cylinder is in its center, so each particle instance of the cylinder is exactly half on the top and half on the bottom.
To set the origin to one end:

Select the cylinder and enter edit mode (Tab)

Select one end of it and press ShiftS&gt; Cursor to selected:


Exit edit mode (Tab) and press CtrlShiftAltC&gt; Origin to 3D cursor: